It depends which airline you're flying.

In my experience, Terminal 7 (BA, UA, Icelandair) is particularly speedy. My recent experiences at Delta (Terminal 3) have been quick too. It's really just American (Terminal 8) where it's been slow.

There are a few things that can help you...
You can walk between Terminals 1, 2, 3, and 4 or between Terminals 6 and 7. If you CAN walk, be sure to do it. It's much, much faster than the bus.

Use carry-ons or interline your bags. That way you can get through JFK unencumbered by checked baggage.

If you don't have checked bags, you can check in for your Delta flight using an automated kiosk; the lines for domestic check-in can be very long in the afternoon.

Finally, the "red coats"--agents handling the check-in lobby at Delta are usually very helpful. If you're running late, let them know and they can get you on your way.

Bon voyage!

Mats (former JFK employee)